If you print over USB, you can often adjust speed/extrusion settings on the fly, depending on your host program. If you print via SD card, you are less liable to get slowdown issues on models with lots of high resolution arcs, which can overwhelm the USB transfer speed. Printing via USB makes your print success reliant on your computer staying awake, not stalling on external drive spinup, etc, unless you use something like OctoPrint on a dedicated computer. It is one less step to print using USB.

I've been bitten in the arse once to many times trying to print via USB so I print mainly via the SD card now. (unless it's something quick say under an hour I still chance it now and again and use the USB.)